Journal: Briefings in Bioinformatics

Article Title: ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing

doi: 10.1093/bib/bbae435

Figure Lengend Snippet: The sliding window sampling with 3-fold tiling and a window size of 3000 achieved better performance. (A) A schematic diagram illustrates sliding window sampling, with examples depicted for strides of 1 and 0.5 times the window size, aimed at sampling nanopore sequencing current signals. Larger tiling-folds were achieved through the reduction of strides. (B, C) The median and mean accuracies of ReadCurrent, derived from training inputs with varying tiling-folds (B) and sliding window sizes (C), were assessed across seven datasets, excluding the public SARS-CoV-2 dataset due to its insufficiently short read lengths.

Article Snippet: Ten synthetic SARS-CoV-2 RNA standards (Twist Bioscience, South San Francisco, USA, as detailed in ) initially underwent reverse transcription before being amplified using the QuantiTect Whole Transcriptome Kit (Qiagen, Duesseldorf, Germany) with random primers.

Techniques: Sampling, Nanopore Sequencing, Derivative Assay

Journal: Heliyon

Article Title: Public health use and lessons learned from a statewide SARS-CoV-2 wastewater monitoring program (MiNET)

doi: 10.1016/j.heliyon.2024.e35790

Figure Lengend Snippet: Summary results of the training validation exercise for 10 trained MiNET labs using a separated box and whiskers plot. SARS CoV-2 gene copy per reaction results for blind sample analysis (n = 1, for triplicate analysis of 3 targets N1, N2 and E) for labs A-J.

Article Snippet: Synthetic SARS-CoV-2 RNA purchased from ATCC (ATCC VR-3276SD), and RNA extracted from the Phi6 bacteriophage (internal control assay) were used as positive controls.

Techniques:

Journal: Heliyon

Article Title: Public health use and lessons learned from a statewide SARS-CoV-2 wastewater monitoring program (MiNET)

doi: 10.1016/j.heliyon.2024.e35790

Figure Lengend Snippet: Monthly SARS CoV-2 percent positives for WWTP, SS and BL sites over the 2020 monitoring period. WWTP sites were monitored between April–December 2020, SS sites May–December 2020 and BL sites from September to December 2020. Percent positives at the WWTP sites ranged between 13 and 100 %, SS sites between 20 and 58 % and BL sites between 37 and 56 %.

Article Snippet: Synthetic SARS-CoV-2 RNA purchased from ATCC (ATCC VR-3276SD), and RNA extracted from the Phi6 bacteriophage (internal control assay) were used as positive controls.

Techniques:

Journal: Heliyon

Article Title: Public health use and lessons learned from a statewide SARS-CoV-2 wastewater monitoring program (MiNET)

doi: 10.1016/j.heliyon.2024.e35790

Figure Lengend Snippet: SARS CoV-2 N1 concentrations correlating a moving average with various lags (rho) with weekly moving average of confirmed cases and positivity rates in Michigan (September–December 2020). County-level incidence rate was computed as the ratio of the number of confirmed cases over county population. County-level positivity rate was obtained by the ratio of the number of positive tests over the number of total tests. The wastewater for datasets Mp and Mp_wwtp showed positive correlations with case incidence rate peaking at a lag of 16 days (rho = 0.866 , p < 0.05 ) for Mp and 12 days (rho = 0.878 , p < 0.05 ) for Mp_wwtp. The wastewater for datasets Mp and Mp_wwtp showed positive correlations with case positivity rates peaking at a lag of 24 days (rho = 0.887 , p < 0.05 ) for Mp and 21 days (rho = 0.870 , p < 0.05 ) for Mp_wwtp.

Article Snippet: Synthetic SARS-CoV-2 RNA purchased from ATCC (ATCC VR-3276SD), and RNA extracted from the Phi6 bacteriophage (internal control assay) were used as positive controls.

Techniques:

Journal: Nature Communications

Article Title: Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

doi: 10.1038/s41467-024-49957-9

Figure Lengend Snippet: a The input of Olivar consists of three components: the targeted sequence, a BLAST database built with non-targeted sequences, and single nucleotide polymorphisms (SNPs) to be avoided by primers. Based on the provided inputs, a risk score is calculated for each nucleotide of the targeted sequence. Primer design regions are optimized according to the array of risk scores. One or more primer candidates are generated for each primer design region, and the primer set with minimum primer dimerization is selected with the previously published algorithm SADDLE. b A primer design region (PDR) is a short region (40nt by default) on the targeted genome. A pair of PDRs (blue or orange solid lines) covers the genomic region between them, and a valid set of PDRs should cover the whole targeted genome. Primer candidates (blue dashed lines) are generated from each PDR by SADDLE. PDRs are assigned into two pools (pool 1 in blue and pool 2 in orange) to avoid overlapping amplicons. c A risk array consists of four components: SNPs, extreme GC content, low sequence complexity and non-specificity, and all of them are calculated for each nucleotide of target and range between 0 and 1. The final risk is calculated as the weighted sum of the four risk components. d An example of the risk landscape of the SARS-CoV-2 genome, as well as primers designed by Olivar. The beginning of the S gene is shown, and each risk component is shown in a different color. Different risk components shown in the figure are stacked together instead of overlapping. Primers are assigned into two pools to avoid overlapping amplicons. Together the two pools cover the whole genome.

Article Snippet: We first tested both primer sets on synthetic SARS-CoV-2 RNA samples (Twist Bioscience), with different RNA concentrations, as determined by the Ct value from quantitative real-time PCR (qPCR) targeting the N gene.

Techniques: Sequencing, Generated

Journal: Nature Communications

Article Title: Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

doi: 10.1038/s41467-024-49957-9

Figure Lengend Snippet: a Starting from the 5' end of the targeted sequence, a pair of PDRs is randomly generated. The length of each PDR is fixed to 40nt. Given that PDRs should not overlap with each other, as well as the desired range of amplicon length, a PDR must fall into a certain region of the targeted sequence, as indicated by the green box. The risk of each 40-mer within this region is calculated as the sum of all single nucleotide risk. Low risk 40-mers (≤ X th percentile) are considered as candidate PDRs and the next PDR is randomly selected among them. PDRs are repeatedly generated until there is no space for another pair of PDRs, and the total risk of the PDR set is calculated. The whole process is repeated N times, with N determined by desired amplicon length and the length of targeted sequence, and the PDR set with the lowest total risk is selected for downstream design. b, c Tuning the threshold for determining candidate PDRs, with SARS-CoV-2 genome as the targeted sequence. Detailed description of other design parameters can be found in the methods section. X is set as 30 for following designs. b For each percentile threshold, 35,584 PDR sets are generated, and their Loss is sorted. c For each percentile threshold, the PDR set with the lowest Loss is selected and the risk of each PDR is shown.

Article Snippet: We first tested both primer sets on synthetic SARS-CoV-2 RNA samples (Twist Bioscience), with different RNA concentrations, as determined by the Ct value from quantitative real-time PCR (qPCR) targeting the N gene.

Techniques: Sequencing, Generated, Amplification